scholarly journals The setting for the origin of life: a geological– geochemical perspective

2018 ◽  
Vol 40 (6) ◽  
pp. 18-21
Author(s):  
Martin J. Van Kranendonk
Keyword(s):  
Amino Acids ◽  
Origin Of Life ◽  
Lipid Membranes ◽  
Organic Molecule ◽  
Organic Geochemistry ◽  
Building Blocks ◽  
Dna Molecules ◽  
Inorganic Geochemistry ◽  
The Origin Of Life ◽  
Rna And Dna

There are many different scientific aspects involved in the challenge of understanding the origin of life (OoL). These include organic geochemistry – how to make RNA and DNA molecules from the simple organic building blocks delivered from space in the form of amino acids and some other compounds. Other aspects involve the study of inorganic geochemistry – how elements are made available to promote organic molecule complexification, under what conditions will lipid membranes form and how to bring together the different components that make a functioning cell.

scholarly journals The Origin of the Information System in the RNA/Protein World: A Simulation Model of the Evolution of Translation and the Genetic Code

2018 ◽  
Author(s):  
Sankar Chatterjee ◽  
Surya Yadav
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Origin Of Life ◽  
Building Blocks ◽  
Translation Machinery ◽  
Crater Lakes ◽  
Universal Genetic Code ◽  
Protein World ◽  
The Origin Of Life

The Late Heavy Bombardment Period (4.1 to 3.8 billion years ago) of heightened impact cratering activity on young Earth is likely the driving force for the origin of life. During the Eoarchean, asteroids such as carbonaceous chondrites delivered the building blocks of life and water to early Earth. Asteroid collisions created innumerable hydrothermal crater lakes in the Eoarchean crust which inadvertently became the perfect cradle for prebiotic chemistry. These hydrothermal crater lakes were filled with cosmic water and the building blocks of life. forming a thick prebiotic soup. The unique combination of exogenous delivery of extraterrestrial building blocks of life, and the endogenous biosynthesis in hydrothermal impact crater lakes very likely gave rise to life. A new symbiotic model for the origin of life within the hydrothermal crater lakes is here proposed. In this scenario, life arose around four billion years ago through five hierarchical stages of increasing molecular complexity: cosmic, geologic, chemical, information, and biological. During the prebiotic synthesis, membranes first appeared in the hydrothermal crater lakes, followed by the simultaneous origin of RNA and protein molecules, creating the RNA/protein world. These proteins were noncoded protein enzymes that facilitated chemical reactions. RNA molecules formed in the hydrothermal crater basin by polymerization of the nucleotides on the montmorillonite mineral substrate. Similarly, the initial synthesis of abiotic protein enzymes was mediated by the condensation of amino acids on pyrite surfaces. The regular wet-dry cycles within the crater lakes assisted further concentration, condensation, and polymerization of the RNAs and proteins. Lipid membranes randomly encapsulated amino acids, RNA, and protein molecules from the prebiotic soup to initiate a molecular symbiosis inside the protocells, this led to the hierarchical emergence of several cell components. As the role of protein enzymes became essential for catalytic process in the RNA/protein world, Darwinian selection from noncoded to coded protein synthesis led to translation systems and the genetic code, heralding the information stage. In this stage, the biochemical pathways suggest the successive emergence of translation machineries such as tRNAs, aaRS, mRNAs, and of ribosomes for protein synthesis. The molecular attraction between tRNA and amino acid led to the emergence of translation machinery and the genetic code.  tRNA is an ancient molecule that created mRNA for the purpose of storing amino acid information like a digital strip. Each mRNA strand became the storage device for genetic information that encoded the amino acid sequences in triplet nucleotides. As information became available in the digital languages of the codon within mRNA, biosynthesis became less random and more organized and directional. The original translation machinery was simpler before the emergence of the ribosome than that of today. We review three main concepts on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and adaptive theory. We believe that these three theories are not mutually exclusive, but are compatible with our coevolution model of translations machines and the genetic code. We suggest biosynthetic pathways as the origin of the translation machine that provided the framework for the origin of the genetic code. During translation, the genetic code developed in three stages coincident with the refinement of the translation machinery: GNC code with four codons and four amino acids during interactions of pre-tRNA/pre-aaRS /pre-mRNA, SNS code consisting of 16 codons and 10 amino acids appeared during the tRNA/aaRS/mRNA interaction, and finally the universal genetic code evolved with the emergence of the tRNA/aaRS/mRNA/ribosome machine. The universal code consists of 64 codons and 20 amino acids, with a redundancy that minimizes errors in translation. To address the question of the origin of the biological information system in the RNA/protein world, we converted letter codons into numerical codons in the Universal Genetic Code Table. We developed a software called CATI (Codon-Amino Acid-Translator-Imitator) to translate randomly chosen numerical codons into corresponding amino acids and vice versa, gaining insight into how translation might have worked in the RNA/protein world. We simulated the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. We used AnyLogic software to simulate and visualize the evolution of the translation machines and the genetic code. We conclude that the emergence of the information age from the RNA/protein world was a watershed event in the origin of life about four billion years ago.

Photochemical Evolution of Interstellar/Precometary Organic Material

1997 ◽  
Vol 161 ◽  
pp. 23-47 ◽  
Author(s):  
Louis J. Allamandola ◽  
Max P. Bernstein ◽  
Scott A. Sandford
Keyword(s):  
Origin Of Life ◽  
Building Blocks ◽  
Complex Species ◽  
Infrared Observations ◽  
Interstellar Ice ◽  
Polycyclic Aromatic ◽  
Ultraviolet Photolysis ◽  
The Origin Of Life ◽  
Simple Molecules ◽  
Complex Organic

AbstractInfrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Since comets are thought to be a major source of the volatiles on the primative earth, their organic inventory is of central importance to questions concerning the origin of life. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, CH4, H2, and probably some NH3and H2CO, as well as more complex species including nitriles, ketones, and esters. The evidence for these, as well as carbonrich materials such as polycyclic aromatic hydrocarbons (PAHs), microdiamonds, and amorphous carbon is briefly reviewed. This is followed by a detailed summary of interstellar/precometary ice photochemical evolution based on laboratory studies of realistic polar ice analogs. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(= O)NH2(formamide), CH3C(= O)NH2(acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including polyoxymethylene and related species (POMs), amides, and ketones. The ready formation of these organic species from simple starting mixtures, the ice chemistry that ensues when these ices are mildly warmed, plus the observation that the more complex refractory photoproducts show lipid-like behavior and readily self organize into droplets upon exposure to liquid water suggest that comets may have played an important role in the origin of life.

General discussion after session V

1988 ◽  
Vol 325 (1587) ◽  
pp. 611-618 ◽  
Keyword(s):  
Origin Of Life ◽  
Time Perspective ◽  
Applied Mathematics ◽  
Building Blocks ◽  
Living Systems ◽  
Organic Chemical ◽  
General Terms ◽  
The Earth ◽  
The Origin Of Life ◽  
Emergence Of Life

N. C. Wickramasinghe ( Department of Applied Mathematics and Astronomy, University College, Cardiff, U. K. ). The question of the origin of life is, of course, one of the most important scientific questions and it is also one of the most difficult. One is inevitably faced here with a situation where there are very few empirical facts of direct relevance and perhaps no facts relating to the actual transition from organic material to material that can even remotely be described as living. The time perspective of events that relate to this problem has already been presented by Dr Chang. Uncertainty still persists as to the actual first moment of the origin or the emergence of life on the Earth. At some time between 3800 and 3300 Ma BP the first microscopic living systems seem to have emerged. There is a definite moment in time corresponding to a sudden appearance of cellular-type living systems. Now, traditionally the evolution of carbonaceous compounds which led to the emergence of life on Earth could be divided into three principal steps and I shall just remind you what those steps are. The first step is the production of chemical building blocks that lead to the origin of the organic molecules necessary as a prerequisite for the evolution of life. Step two can be described in general terms as prebiotic evolution, the arrangement of these chemical units into some kind of sequence of precursor systems that come almost up to life but not quite; and then stage three is the early biological evolution which actually effects the transition from proto-cellular organic-type forms into truly cellular living systems. The transition is from organic chemistry, prebiotic chemistry to biochemistry. Those are the three principal stages that have been defined by traditional workers in the field, the people who, as Dr Chang said, have had the courage to make these queries and attempt to answer them. Ever since the classic experiments where organic materials were synthesized in the laboratory a few decades back, it was thought that the first step, the production of organic chemical units, is important for the origin of life on the Earth, and that this had to take place in some location on the Earth itself.

Autocatalytic chemical networks preceded proteins and RNA in evolution

2019 ◽  
Author(s):  
Joana C. Xavier ◽  
Wim Hordijk ◽  
Stuart Kauffman ◽  
Mike Steel ◽  
William F. Martin
Keyword(s):  
Amino Acids ◽  
Origin Of Life ◽  
Small Molecule ◽  
Metabolic Networks ◽  
Early Earth ◽  
Prebiotic Evolution ◽  
Biochemical Evolution ◽  
The Origin Of Life ◽  
Acids And Bases ◽  
Open Question

AbstractModern cells embody metabolic networks containing thousands of elements and form autocatalytic molecule sets that produce copies of themselves. How the first self-sustaining metabolic networks arose at life’ s origin is a major open question. Autocatalytic molecule sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here we identify reflexively autocatalytic food-generated networks (RAFs)—self-sustaining networks that collectively catalyze all their reactions—embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H2 and CO2 generate amino acids and bases, the monomeric components of protein and RNA, and acetyl-CoA, but amino acids and bases do not generate metabolic RAFs, indicating that small-molecule catalysis preceded polymers in biochemical evolution. RAFs uncover intermediate stages in the origin of metabolic networks, narrowing the gaps between early-Earth chemistry and life.

The sulfocyanic theory on the origin of life: towards a critical reappraisal of an autotrophic theory

2003 ◽  
Vol 2 (4) ◽  
pp. 301-306 ◽  
Author(s):  
L. Perezgasga ◽  
E. Silva ◽  
A. Lazcano ◽  
A. Negrón-Mendoza
Keyword(s):  
Amino Acids ◽  
Origin Of Life ◽  
Raw Materials ◽  
Total Yield ◽  
Historical Analysis ◽  
Preliminary Identification ◽  
Chemical Significance ◽  
The Origin Of Life ◽  
Materials Used ◽  
Emergence Of Life

In the early 1930s, Alfonso L. Herrera proposed his so-called sulfocyanic theory on the origin of life, an autotrophic proposal on the first living beings according to which NH4SCN and H2CO acted as raw materials for the synthesis of bio-organic compounds inside primordial photosynthetic protoplasmic structures. Although the work of Herrera is frequently cited in historical analysis of the development of the origin of life studies, very little attention has been given to the chemical significance of the reactions he published. In this paper we report the results of our search for amino acids obtained from a reactive mixture used by Herrera from 1933 onwards. Chromatograms using the high-pressure liquid chromatography (HPLC) technique suggest the presence of several amino acids, the total yield being 2% of the initial thiocyanate used. Preliminary identification based on HPLC retention times suggests the presence of glycine, alanine, cysteine and methionine. Alanine was the most abundant amino acid in all samples of fractionated material analysed. Although the starting materials used by Herrera were determined by his autotrophic hypothesis on the origin of cells, our results show that his experiments may provide insights into the abiotic synthesis of sulfur-containing amino acids within the framework of a heterotrophic emergence of life.

scholarly journals An optimal degree of physical and chemical heterogeneity for the origin of life?

2011 ◽  
Vol 366 (1580) ◽  
pp. 2894-2901 ◽  
Author(s):  
Jack W. Szostak
Keyword(s):  
Nucleic Acid ◽  
Origin Of Life ◽  
Self Assembly ◽  
Building Blocks ◽  
Reaction Products ◽  
Amphiphilic Molecules ◽  
Essential Components ◽  
The Origin Of Life ◽  
Chemical Inputs ◽  
Physical And Chemical

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.

Chemical evolution toward the origin of life

2007 ◽  
Vol 79 (12) ◽  
pp. 2101-2117 ◽  
Author(s):  
Daniel Fitz ◽  
Hannes Reiner ◽  
Bernd Michael Rode
Keyword(s):  
Chemical Evolution ◽  
Rna World ◽  
Early Stage ◽  
Building Blocks ◽  
Point Of View ◽  
Peptide Formation ◽  
The Origin Of Life ◽  
Life On Earth ◽  
Primordial Earth ◽  
Rna And Dna

Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.

scholarly journals Search for water and life's building blocks in the universe: A summary

2015 ◽  
Vol 11 (A29B) ◽  
pp. 436-440
Author(s):  
Edwin A. Bergin
Keyword(s):  
Origin Of Life ◽  
Radioactive Decay ◽  
Building Blocks ◽  
The Origin Of Life ◽  
The Right ◽  
The Universe

AbstractWater and organics need to be supplied to terrestrial worlds like our own to provide the essential compounds required for the origin of life. These molecules form initially during the earliest stages of stellar birth, are supplied by collapse to the planet-forming disk predominantly as ice, and may undergo significant processing during this collapse and within large planetesimals that are heated via radioactive decay. Water and organic carriers can be quite volatile, thus their survival as ices within rocks is not preordained. In this focus meeting our goal is to bring together astronomers, cosmochemists, planetary scientists, chemical physicists, and spectroscopists who each explore individual aspects of this problem. In this summary we discuss some of the main themes that appeared in the meeting. Ultimately, cross-field collaboration is needed to provide greater understanding of the likelihood that terrestrial worlds form with these key compounds readily available on their surfaces – and are hence habitable if present at the right distance from the star.

The first step from molecules to life: Formation of large random molecules acting as micro-environments

2020 ◽  
Author(s):  
Saibal Mitra
Keyword(s):  
Molecular Biology ◽  
Origin Of Life ◽  
Ultraviolet Irradiation ◽  
Building Blocks ◽  
Percolation Process ◽  
Von Neumann ◽  
Percolation Clusters ◽  
Period 2 ◽  
Interstellar Ice ◽  
The Origin Of Life

<p>The mathematician John von Neumann, through his work on universal constructors, discovered<br />a generalized version of the central dogma of molecular biology biology in the 1940s, long  <br />before the biological version had been discovered. While his discovery played no role in the  <br />development of molecular biology, we may benefit from a similar mathematical approach to find  <br />clues on the origin of life. This then involves addressing those problems in the field that  <br />do not depend on the details of organic chemistry. We can then consider a general set of  <br />models that describe machines capable of self-maintenance and self-replication formulated in  <br />terms of a set of building blocks and their interactions. </p> <p>The analogue of the origin of life problem is then to explain how one can get to such  <br />machines starting from a set of only building blocks. A fundamental obstacle one then faces  <br />is the limit on the complexity of low fidelity replicating systems, preventing building  <br />blocks from getting assembled randomly into low fidelity machines which can then improve due  <br />to natural selection [1]. A generic way out of this problem is for the entire ecosystem of  <br />machines to have been encapsulated in a micro-structure with fixed inner surface features  <br />that would have boosted the fidelity [2]. Such micro-structures could have formed as a result  <br />of the random assembly of building blocks, leading to so-called percolation clusters [2].</p> <p>This then leads us to consider how in the real world a percolation process involving the  <br />random assembly of organic molecules can be realized. A well studied process in the  <br />literature is the assembly of organic compounds in ice grains due to UV radiation and heating  <br />events [3,4,5]. This same process will also lead to the percolation process if it proceeds  <br />for a sufficiently long period [2].</p> <p>In this talk I will discuss the percolation process in more detail than has been done in [2],  <br />explaining how it leads to the necessary symmetry breakings such as the origin of chiral  <br />molecules needed to explain the origin of life.   </p> <p> </p> <p>[1] Eigen, M., 1971. Self-organization of matter and the evolution of biological  <br />macromolecules. Naturwissenschaften 58, 465-523.</p> <p>[2] Mitra, S., 2019. Percolation clusters of organics in interstellar ice grains as the  <br />incubators of life, Progress in Biophysics and Molecular Biology 149, 33-38.</p> <p>[3] Ciesla, F., and Sandford.,S., 2012. Organic Synthesis via Irradiation and Warming of Ice  <br />Grains in the Solar Nebula. Science 336, 452-454.</p> <p>[4] Muñoz Caro, G., et al., 2002. Amino acids from ultraviolet irradiation of interstellar ice  <br />analogues. Nature 416, 403-406.</p> <p>[5]  Meinert, C,., et al., 2016. Ribose and related sugars from ultraviolet irradiation of  <br />interstellar ice analogs. Science 352, 208-212.</p>

Sign in / Sign up

Export Citation Format

Share Document